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- PDB-4ri2: Crystal structure of the photoprotective protein PsbS from spinach -

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Basic information

Entry
Database: PDB / ID: 4ri2
TitleCrystal structure of the photoprotective protein PsbS from spinach
ComponentsPhotosystem II 22 kDa protein, chloroplastic
KeywordsMEMBRANE PROTEIN / transmembrane helices / photo protection / pigment binding
Function / homology
Function and homology information


photosystem II / chloroplast thylakoid membrane / photosynthesis / phosphoprotein binding / identical protein binding
Similarity search - Function
Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
CHLOROPHYLL A / : / Photosystem II 22 kDa protein, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.35 Å
AuthorsFan, M. / Li, M. / Chang, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structures of the PsbS protein essential for photoprotection in plants.
Authors: Fan, M. / Li, M. / Liu, Z. / Cao, P. / Pan, X. / Zhang, H. / Zhao, X. / Zhang, J. / Chang, W.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II 22 kDa protein, chloroplastic
B: Photosystem II 22 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4168
Polymers45,0962
Non-polymers2,3206
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-31 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.999, 77.537, 93.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Photosystem II 22 kDa protein, chloroplastic / CP22


Mass: 22548.221 Da / Num. of mol.: 2 / Fragment: UNP residues 63-274 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q02060
#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM sodium acetate, 25% PEG 300, 1% ethyl acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 22287 / Num. obs: 22232 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.35→2.43 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.35→29.801 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 27.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 1991 8.96 %
Rwork0.2295 --
obs0.2327 22232 99.06 %
all-22287 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→29.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 150 43 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042755
X-RAY DIFFRACTIONf_angle_d0.9153724
X-RAY DIFFRACTIONf_dihedral_angle_d15.355992
X-RAY DIFFRACTIONf_chiral_restr0.059439
X-RAY DIFFRACTIONf_plane_restr0.003458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40420.31621330.26771364X-RAY DIFFRACTION95
2.4042-2.46910.31291530.25061400X-RAY DIFFRACTION100
2.4691-2.54180.28761240.24581418X-RAY DIFFRACTION100
2.5418-2.62380.32891450.23231455X-RAY DIFFRACTION100
2.6238-2.71750.28981450.22081440X-RAY DIFFRACTION100
2.7175-2.82620.25791490.21561440X-RAY DIFFRACTION100
2.8262-2.95470.30431370.22521449X-RAY DIFFRACTION100
2.9547-3.11030.31181510.23221446X-RAY DIFFRACTION100
3.1103-3.3050.24591420.22341450X-RAY DIFFRACTION100
3.305-3.55980.24661340.21541467X-RAY DIFFRACTION100
3.5598-3.91730.23411520.21711459X-RAY DIFFRACTION100
3.9173-4.48250.24711330.21891476X-RAY DIFFRACTION100
4.4825-5.64120.25721480.23891492X-RAY DIFFRACTION100
5.6412-29.80350.27011450.24311485X-RAY DIFFRACTION94

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